Correlation between gene mutation status and molecular subtypes
Uterine Carcinosarcoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C13R0RK9
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13R0RK9
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 9 genes and 8 molecular subtypes across 57 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.

  • PTEN mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 9 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 2 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
PTEN 11 (19%) 46 0.0123
(0.833) 		0.000216
(0.0156) 		0.00212
(0.151) 		0.00433
(0.303) 		0.096
(1.00) 		0.00872
(0.602) 		0.0237
(1.00) 		0.0241
(1.00)
FBXW7 22 (39%) 35 0.0511
(1.00) 		0.714
(1.00) 		0.595
(1.00) 		0.494
(1.00) 		0.441
(1.00) 		1
(1.00) 		0.938
(1.00) 		0.737
(1.00)
KRAS 7 (12%) 50 0.32
(1.00) 		0.0187
(1.00) 		0.0323
(1.00) 		0.0264
(1.00) 		0.463
(1.00) 		0.494
(1.00) 		0.513
(1.00) 		0.322
(1.00)
TP53 51 (89%) 6 0.331
(1.00) 		0.591
(1.00) 		0.877
(1.00) 		0.822
(1.00) 		1
(1.00) 		0.699
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 20 (35%) 37 0.267
(1.00) 		0.875
(1.00) 		0.365
(1.00) 		0.303
(1.00) 		0.105
(1.00) 		0.0268
(1.00) 		0.162
(1.00) 		0.0274
(1.00)
PPP2R1A 16 (28%) 41 1
(1.00) 		0.701
(1.00) 		0.584
(1.00) 		0.852
(1.00) 		0.56
(1.00) 		0.635
(1.00) 		0.234
(1.00) 		1
(1.00)
PIK3R1 6 (11%) 51 0.856
(1.00) 		0.95
(1.00) 		0.544
(1.00) 		0.592
(1.00) 		0.425
(1.00) 		0.705
(1.00) 		0.744
(1.00) 		0.459
(1.00)
ZBTB7B 6 (11%) 51 0.483
(1.00) 		0.95
(1.00) 		1
(1.00) 		1
(1.00) 		0.0978
(1.00) 		0.197
(1.00) 		0.15
(1.00) 		0.29
(1.00)
RB1 6 (11%) 51 0.541
(1.00) 		0.121
(1.00) 		0.08
(1.00) 		0.0401
(1.00) 		0.835
(1.00) 		0.484
(1.00) 		0.918
(1.00) 		0.712
(1.00)
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0511 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
FBXW7 MUTATED 12 9 1
FBXW7 WILD-TYPE 10 15 9
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.714 (Chi-square test), Q value = 1

Table S2.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
FBXW7 MUTATED 6 4 4 3 5
FBXW7 WILD-TYPE 6 5 6 10 8
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.595 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
FBXW7 MUTATED 7 8 5 2
FBXW7 WILD-TYPE 8 12 7 8
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
FBXW7 MUTATED 8 4 8 2
FBXW7 WILD-TYPE 7 7 14 7
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
FBXW7 MUTATED 5 8 3 6
FBXW7 WILD-TYPE 6 14 1 13
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
FBXW7 MUTATED 0 11 11
FBXW7 WILD-TYPE 1 16 17
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
FBXW7 MUTATED 5 9 2 6
FBXW7 WILD-TYPE 6 14 3 11
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.737 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
FBXW7 MUTATED 0 11 11
FBXW7 WILD-TYPE 1 14 19
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 1

Table S9.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
KRAS MUTATED 2 5 0
KRAS WILD-TYPE 20 19 10
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0187 (Chi-square test), Q value = 1

Table S10.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
KRAS MUTATED 0 1 1 0 5
KRAS WILD-TYPE 12 8 9 13 8

Figure S1.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0323 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
KRAS MUTATED 0 3 4 0
KRAS WILD-TYPE 15 17 8 10

Figure S2.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0264 (Fisher's exact test), Q value = 1

Table S12.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
KRAS MUTATED 0 4 3 0
KRAS WILD-TYPE 15 7 19 9

Figure S3.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
KRAS MUTATED 1 4 1 1
KRAS WILD-TYPE 10 18 3 18
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
KRAS MUTATED 0 2 5
KRAS WILD-TYPE 1 25 23
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
KRAS MUTATED 1 5 0 1
KRAS WILD-TYPE 10 18 5 16
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
KRAS MUTATED 0 5 2
KRAS WILD-TYPE 1 20 28
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
TP53 MUTATED 21 21 8
TP53 WILD-TYPE 1 3 2
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.591 (Chi-square test), Q value = 1

Table S18.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
TP53 MUTATED 12 8 8 12 11
TP53 WILD-TYPE 0 1 2 1 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S19.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
TP53 MUTATED 14 18 10 9
TP53 WILD-TYPE 1 2 2 1
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S20.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
TP53 MUTATED 14 9 20 8
TP53 WILD-TYPE 1 2 2 1
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
TP53 MUTATED 10 20 4 17
TP53 WILD-TYPE 1 2 0 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
TP53 MUTATED 1 24 26
TP53 WILD-TYPE 0 3 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
TP53 MUTATED 10 21 5 15
TP53 WILD-TYPE 1 2 0 2
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
TP53 MUTATED 1 23 27
TP53 WILD-TYPE 0 2 3
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 1

Table S25.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
PIK3CA MUTATED 5 11 3
PIK3CA WILD-TYPE 17 13 7
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.875 (Chi-square test), Q value = 1

Table S26.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
PIK3CA MUTATED 4 3 5 4 4
PIK3CA WILD-TYPE 8 6 5 9 9
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 1

Table S27.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PIK3CA MUTATED 5 10 3 2
PIK3CA WILD-TYPE 10 10 9 8
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S28.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
PIK3CA MUTATED 6 3 10 1
PIK3CA WILD-TYPE 9 8 12 8
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PIK3CA MUTATED 4 4 2 10
PIK3CA WILD-TYPE 7 18 2 9
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
PIK3CA MUTATED 1 13 6
PIK3CA WILD-TYPE 0 14 22

Figure S4.  Get High-res Image Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
PIK3CA MUTATED 5 5 1 9
PIK3CA WILD-TYPE 6 18 4 8
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
PIK3CA MUTATED 1 5 14
PIK3CA WILD-TYPE 0 20 16

Figure S5.  Get High-res Image Gene #4: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S33.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
PPP2R1A MUTATED 6 7 3
PPP2R1A WILD-TYPE 16 17 7
'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.701 (Chi-square test), Q value = 1

Table S34.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
PPP2R1A MUTATED 4 3 4 3 2
PPP2R1A WILD-TYPE 8 6 6 10 11
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S35.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PPP2R1A MUTATED 6 5 2 3
PPP2R1A WILD-TYPE 9 15 10 7
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S36.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
PPP2R1A MUTATED 5 2 6 3
PPP2R1A WILD-TYPE 10 9 16 6
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PPP2R1A MUTATED 5 5 1 5
PPP2R1A WILD-TYPE 6 17 3 14
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.635 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
PPP2R1A MUTATED 0 9 7
PPP2R1A WILD-TYPE 1 18 21
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
PPP2R1A MUTATED 6 5 1 4
PPP2R1A WILD-TYPE 5 18 4 13
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
PPP2R1A MUTATED 0 7 9
PPP2R1A WILD-TYPE 1 18 21
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0123 (Fisher's exact test), Q value = 0.83

Table S41.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
PTEN MUTATED 1 9 1
PTEN WILD-TYPE 21 15 9

Figure S6.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.000216 (Chi-square test), Q value = 0.016

Table S42.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
PTEN MUTATED 0 0 6 5 0
PTEN WILD-TYPE 12 9 4 8 13

Figure S7.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00212 (Fisher's exact test), Q value = 0.15

Table S43.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PTEN MUTATED 0 8 0 3
PTEN WILD-TYPE 15 12 12 7

Figure S8.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.3

Table S44.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
PTEN MUTATED 0 0 8 3
PTEN WILD-TYPE 15 11 14 6

Figure S9.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.096 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PTEN MUTATED 2 1 1 6
PTEN WILD-TYPE 9 21 3 13
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00872 (Fisher's exact test), Q value = 0.6

Table S46.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
PTEN MUTATED 0 9 1
PTEN WILD-TYPE 1 18 27

Figure S10.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
PTEN MUTATED 1 1 2 6
PTEN WILD-TYPE 10 22 3 11

Figure S11.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0241 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
PTEN MUTATED 0 1 9
PTEN WILD-TYPE 1 24 21

Figure S12.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S49.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
PIK3R1 MUTATED 3 2 1
PIK3R1 WILD-TYPE 19 22 9
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.95 (Chi-square test), Q value = 1

Table S50.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
PIK3R1 MUTATED 2 1 1 1 1
PIK3R1 WILD-TYPE 10 8 9 12 12
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S51.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
PIK3R1 MUTATED 3 2 1 0
PIK3R1 WILD-TYPE 12 18 11 10
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S52.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
PIK3R1 MUTATED 3 1 2 0
PIK3R1 WILD-TYPE 12 10 20 9
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S53.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
PIK3R1 MUTATED 2 2 1 1
PIK3R1 WILD-TYPE 9 20 3 18
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S54.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
PIK3R1 MUTATED 0 2 4
PIK3R1 WILD-TYPE 1 25 24
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S55.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
PIK3R1 MUTATED 2 3 0 1
PIK3R1 WILD-TYPE 9 20 5 16
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 1

Table S56.  Gene #7: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
PIK3R1 MUTATED 0 4 2
PIK3R1 WILD-TYPE 1 21 28
'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S57.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
ZBTB7B MUTATED 3 1 1
ZBTB7B WILD-TYPE 19 23 9
'ZBTB7B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.95 (Chi-square test), Q value = 1

Table S58.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
ZBTB7B MUTATED 2 1 1 1 1
ZBTB7B WILD-TYPE 10 8 9 12 12
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S59.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
ZBTB7B MUTATED 2 2 1 1
ZBTB7B WILD-TYPE 13 18 11 9
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S60.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
ZBTB7B MUTATED 2 1 2 1
ZBTB7B WILD-TYPE 13 10 20 8
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0978 (Fisher's exact test), Q value = 1

Table S61.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
ZBTB7B MUTATED 1 1 2 2
ZBTB7B WILD-TYPE 10 21 2 17
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 1

Table S62.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
ZBTB7B MUTATED 0 5 1
ZBTB7B WILD-TYPE 1 22 27
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 1

Table S63.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
ZBTB7B MUTATED 1 1 2 2
ZBTB7B WILD-TYPE 10 22 3 15
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 1

Table S64.  Gene #8: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
ZBTB7B MUTATED 0 1 5
ZBTB7B WILD-TYPE 1 24 25
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S65.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 24 10
RB1 MUTATED 2 4 0
RB1 WILD-TYPE 20 20 10
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.121 (Chi-square test), Q value = 1

Table S66.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 12 9 10 13 13
RB1 MUTATED 0 1 3 2 0
RB1 WILD-TYPE 12 8 7 11 13
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.08 (Fisher's exact test), Q value = 1

Table S67.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 20 12 10
RB1 MUTATED 0 4 0 2
RB1 WILD-TYPE 15 16 12 8
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0401 (Fisher's exact test), Q value = 1

Table S68.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 15 11 22 9
RB1 MUTATED 0 0 3 3
RB1 WILD-TYPE 15 11 19 6

Figure S13.  Get High-res Image Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S69.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 22 4 19
RB1 MUTATED 2 2 0 2
RB1 WILD-TYPE 9 20 4 17
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S70.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 27 28
RB1 MUTATED 0 4 2
RB1 WILD-TYPE 1 23 26
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S71.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 11 23 5 17
RB1 MUTATED 1 2 1 2
RB1 WILD-TYPE 10 21 4 15
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.712 (Fisher's exact test), Q value = 1

Table S72.  Gene #9: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 1 25 30
RB1 MUTATED 0 2 4
RB1 WILD-TYPE 1 23 26
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = UCS-TP.transferedmergedcluster.txt

  • Number of patients = 57

  • Number of significantly mutated genes = 9

  • Number of Molecular subtypes = 8

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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